Journal of Molecular Modeling

, Volume 10, Issue 5–6, pp 317–327 | Cite as

Modeling the E. coli 4-hydroxybenzoic acid oligoprenyltransferase (ubiA transferase) and characterization of potential active sites

  • Lars Bräuer
  • Wolfgang Brandt
  • Ludger A. Wessjohann
Original Paper

Abstract

4-Hydroxybenzoate oligoprenyltransferase of E. coli, encoded in the gene ubiA, is an important key enzyme in the biosynthetic pathway to ubiquinone. It catalyzes the prenylation of 4-hydroxybenzoic acid in position 3 using an oligoprenyl diphosphate as a second substrate. Up to now, no X-ray structure of this oligoprenyltransferase or any structurally related enzyme is known. Knowledge of the tertiary structure and possible active sites is, however, essential for understanding the catalysis mechanism and the substrate specificity.

With homology modeling techniques, secondary structure prediction tools, molecular dynamics simulations, and energy optimizations, a model with two putative active sites could be created and refined. One active site selected to be the most likely one for the docking of oligoprenyl diphosphate and 4-hydroxybenzoic acid is located near the N-terminus of the enzyme. It is widely accepted that residues forming an active site are usually evolutionary conserved within a family of enzymes. Multiple alignments of a multitude of related proteins clearly showed 100% conservation of the amino acid residues that form the first putative active site and therefore strongly support this hypothesis. However, an additional highly conserved region in the amino acid sequence of the ubiA enzyme could be detected, which also can be considered a putative (or rudimentary) active site. This site is characterized by a high sequence similarity to the aforementioned site and may give some hints regarding the evolutionary origin of the ubiA enzyme.

Semiempirical quantum mechanical PM3 calculations have been performed to investigate the thermodynamics and kinetics of the catalysis mechanism. These results suggest a near SN1 mechanism for the cleavage of the diphosphate ion from the isoprenyl unit. The 4-hydroxybenzoic acid interestingly appears not to be activated as benzoate anion but rather as phenolate anion to allow attack of the isoprenyl cation to the phenolate, which appeared to be the rate limiting step of the whole process according to our quantum chemical calculations. Our models are a basis for developing inhibitors of this enzyme, which is crucial for bacterial aerobic metabolism.

Figure Structure of the model of ubiA oligoprenyltransferase derived from the photosynthetic reaction center (1PRC). Putative active amino acid residues and substrates are shown as capped sticks to describe their location and geometry in the putative active sites. The violet spheres identify Mg2+.

Keywords

Transferases Prenylation Homology modeling Biocatalysis mechanism 

Abbreviations

3D-PSSM

3D protein secondary structure prediction

4-HB

4-hydroxybenzoic acid (para-hydroxybenzoat)

BLAST

basic local alignment search tool

BLOSUM

blocks substitution matrix

DMAPP

dimethylallyl diphosphate

GOLD

genetic optimization ligand docking

GPP

geranyl diphosphate

HIV

human immunodeficiency virus

MOE

molecular operating environment

OP-PP

octaprenyl diphosphate

PAM

percent accepted mutation

PDB

protein data bank

pHB

para-hydroxybenzoic acid

PM3

parametrized method 3

PP or DPP

diphosphate

PROSA

protein structure analysis

TAFF

tripos associated force field

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Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  • Lars Bräuer
    • 1
  • Wolfgang Brandt
    • 1
  • Ludger A. Wessjohann
    • 1
  1. 1.Department of Bioorganic ChemistryLeibniz Institute of Plant BiochemistryHalleGermany

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